Genetic diversity and population structure assessment of Western Canadian barley cooperative trials

Ludovic J A Capo-Chichi; Ammar Elakhdar; Takahiko Kubo; Joseph Nyachiro; Patricia Juskiw; Flavio Capettini; Jan J Slaski; Guillermo Hernandez Ramirez; Aaron D Beattie

doi:10.3389/fpls.2022.1006719

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials

Front Plant Sci. 2023 Jan 9:13:1006719. doi: 10.3389/fpls.2022.1006719. eCollection 2022.

Authors

Ludovic J A Capo-Chichi¹, Ammar Elakhdar^{2

3}, Takahiko Kubo², Joseph Nyachiro⁴, Patricia Juskiw⁴, Flavio Capettini⁴, Jan J Slaski⁵, Guillermo Hernandez Ramirez¹, Aaron D Beattie⁶

Affiliations

¹ Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.
² Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.
³ Field Crops Research Institute, Agricultural Research Center, Giza, Egypt.
⁴ Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada.
⁵ Ecosystems and Plant Sciences, InnoTech Alberta Inc., Vegreville, AB, Canada.
⁶ Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada.

Abstract

Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r², declined to below the critical r^{2 =} 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

Keywords: Hordeum vulgare L; SNP markers; allelic variability; association mapping; historical datasets; structure.

Grants and funding

This study received funding from the CDC barley breeding program by the Saskatchewan Ministry of Agriculture and the Western Grains Research Foundation Check-off. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication.